My girlfriend, who is Japanese and has thus eaten and cooked a lot more tofu than I have, says that tofu should either be eaten "raw" or well cooked. To be half and half will cause a bad stomach. She last said this to me when I said I only added silken tofu to miso soup just before I eat it.
However, in the last year I started to make my own tofu, so I know that the last heating of the soy milk makes it digestible. Then, for example with silken tofu, the soy milk is steamed/cooked in a bain-marie to produce the silken tofu. So from my experience of eating it with miso soup I've never had a bad stomach (because I'd assume dropping it into hot soup would constitute undercooking) and from my knowledge of the process it is rendered edible at the milk stage.
However, tofu is so ubiquitous in Japan that I find her input hard to dismiss. Does anyone have any insight that would help clarify this.